I did make a change mid game, but it was just a slight playspeed increase. None of the KB's exceed 20 ether
That's strange. What you described was exactly
the same as what happened to me when I had overstuffed Magneto's PS file. Whenever he was present in a full team (didn't seem to happen much when he was solo) and we made it to an enemy loaded area, such as the Cerci tunnels on Genosha, the game would completely soil itself in stupidity. Storm fired off infinite Xtremes, Wolverine would throw non-stop flying kicks, Cyclops behaved like Wolverine, all the enemies would teleport like Nightcrawler, Xavier stood up
and NPCs at the Sanctuary were in combat poses instead of casual idling.
Once I cut down on Magneto's PS file, that nonsense stopped. It was hilarious to watch, but endlessly frustrating when I didn't understand what was causing the glitches.